Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "11.0.21" 2023-10-17; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /data/nyt/Projects/Juicer-Out/2024-02-14_MGNC/Ph_Sasha_Yan/Ph_Nla_homeCS -s NlaIII -y /data/nyt/Databases/hg38/juicer.rs/GRCh38_no_alt_analysis_set_GCA_000001405.15_NlaIII.txt -p /data/nyt/Databases/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.chromsizes -z /data/nyt/Databases/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta -D /data/nyt/MMO/Tools/juicer1.6_compact -t 20                                                                                                                                                                                                                                                                                                                                                                                                                                                
Sequenced Read Pairs:  1,089,883
 Normal Paired: 548,403 (50.32%)
 Chimeric Paired: 401,768 (36.86%)
 Chimeric Ambiguous: 126,093 (11.57%)
 Unmapped: 13,619 (1.25%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 950,171 (87.18%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-02-15T15:31:12,704]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 938,304 (86.09%)
PCR Duplicates: 11,739 (1.08%)
Optical Duplicates: 128 (0.01%)
Library Complexity Estimate: 38,126,384
Intra-fragment Reads: 72,663 (6.67% / 7.74%)
Below MAPQ Threshold: 81,338 (7.46% / 8.67%)
Hi-C Contacts: 856,966 (78.63% / 91.33%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 72% - 28%
 Pair Type intra chrom %(L-I-O-R): 9% - 75% - 8% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 57%
 Cis/all (FF and RR orient): 68.0%
Inter-chromosomal: 118,516  (10.87% / 12.63%)
Intra-chromosomal: 738,450  (67.75% / 78.70%)
Short Range (<20,000bp): 570,160  (52.31% / 60.76%)
Long Range (>20,000bp): 168,290  (15.44% / 17.94%)